Litter dynamics and outwelling of particulate organic matter (POM) was investigated in a subtropical mangrove (Okinawa Island, South Japan) in order to quantify the impact of mangrove POM on adjacent intertidal sediments. A distinct seasonal pattern was found with maximum litter fall during the autumn season, and minimum during winter. Total litter production between sites did not differ significantly. Tall mangroves (average 7 m) did not show any higher contribution to the litter production than short mangroves (average 4 m). The mean annual litter production was 12.95 ± 2.95 t ha−1 (dry weight) with leaf fall contributing more than 70% of the total litter production. Analysis of fatty acids (FAs) in the surface sediments of an adjacent mud flat and sand flat during the winter, spring and autumn seasons indicated that outwelling of POM from the mangrove ecosystem occurs. However, it is spatially restricted to within 300 m from the mangrove forest. The magnitude of the outwelling increased during spring and autumn consistent with the increase in the total litter production. Despite the presence of mangrove-derived organic matter in the estuarine surface sediments, autochthonous sources of organic matter, green macroalgae (Ulva pertusa and Enteromorpha intestinalis), diatoms and bacteria are the main contributors of sedimentary organic matter and ω3 and ω6 PUFAs than mangrove-derived (POM) during winter and spring. While the contribution of mangrove-derived POM to sedimentary organic matter is limited to the autumn season.